methrix_pca {methrix} | R Documentation |
Principal Component Analysis
methrix_pca( m, var = "top", top_var = 1000, ranges = NULL, pheno = NULL, do_plot = TRUE, n_pc = 2 )
m |
Input |
var |
Choose between random CpG sites ('rand') or most variable CpGs ('top'). |
top_var |
Number of variable CpGs to use. Default 1000 Set it to NULL to use all CpGs (which is not recommended due to memory requirements). This option is mutually exclusive with |
ranges |
genomic regions to be summarized. Could be a data.table with 3 columns (chr, start, end) or a |
pheno |
Column name of colData(m). Default NULL. Will be used as a factor to color different groups |
do_plot |
Should a plot be generated? |
n_pc |
Default 2. |
PCA results
data('methrix_data') methrix_pca(methrix_data, do_plot = FALSE)